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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa03LNT0219600.2

AATAAGATCACATCAAATGCCAAATATTATTTTTAGCAATTCATGCTACAAACACTCCTCTGCATAAGGCAGCAATGTCGAGATTGAAATGAAGAAATACAAACATCACTACAAGGAAAATGACAATAAAGCAGCAATGAGCTGCTTACATAGGATCATCCGAAGCAAGCTTGGATACACGATTATTCATAATAGAGACACTCTGATCAAAATCAAATTAAAGCGAAGTCATATGATGGAAACCTAGAGTGTTATTGGCTGAACAAGCAACAAGGATATCCATTCTTTCAGTATTGCAGAATCAGTATATCCATCAATTTTCTTGTACATTGTTTCCATCATGCGTGCAAGGTTAATAACCTGGATAAGCAAGGAAGACGGAATTGAGGTCAATTTTAGGTACTCCTCGTTCATATCTTTCCATGCATTTTCCACATCATTCCACAGTGCTTTAATGGCCTCCTCCTTTGTGCTGTCATACTCTTTCATATAGCAAGTTACAGCGGTAGCAACATTGTTCCTTTCGGTCTCAAACGCATGAGCAACAATGTCATCCATTAGTCGAGAAACAATACATGAATCCTTGACAATTTGAGGAAATCCTGACATCCATATCATAACCTCCTCTGTAACACCTTCTTGAAAAACAACAAAAGCAGTGCAGTTTATTGCCCAATAGAAGCACGTAACTAGTGTGATTTGCAAATGCTCCTTTAATGGGGGAATGTATTTACTATCTCTCCAATCGATTTCTGTTACATAGCCTTTGCATACTTCAGTGATCTATAAAATAAAGTAAGTCAAAGCATATGTACATGAGTGGGCTCTTTGCATATGTATTTTCAAAACACTTAATAATAAACTAATTTACTTTAATAAAATAAACATGTCATGCATGAATACACACATATAATTGAATGGATGGAATGGTGTAATTAAAAGGAAAAAATTACAAAAAAAACTGAGAATATACATACTATATCTTTGATAACATTAACATTCTTCCTTGGTGTTCCTTTTGGGAGTGCACCCTCAATCTCATTCATGGTGCCAAACATAAATTGAGCATATTCCTTGTAACATCTTCCAAGTTGCTCAGCACCCTTTTCATCCCACCGTTGCATCACGTCAGCAAATGGTTGAAGCTCTTTCCAGAGTCCATAATTGTCAAAAGTATCATCATATGGTGTAATAGTTGCTATGAATTTCGCTAGCAACTTCCTAGGCTTTGCATATTCTGGTTCATAATACACACCCAACGCCCAAAAATATGCTTCTGCAGGCCTATGCCTTGCATAGAATAGTTCACGTGGGGACTCTAGCCCATGATACCACTCGCATATTTCTTTGACTTCTTCCCGGTGAAGTCGCTGCAATAAATAAAAGTCAAGTTTTGCTAGCTCAAGTATCATCTCGTTGCACTCCTCCTTATCTTCTTCATACAATGGTATGTAAAGTCTGGCCTCTAACCTCTTCATCCTACGGAAAGATGGTGTCTCAAGAGCATGTCTCACTTTATTAGAGAGTGGTTTCTCAATACAATCCACAATTCTTTTCAATTGATTTGTTGTTTCAACCTGTGCTTCTCGGAGAATTTCTTCATTAGGAGTTCCAAGATGTGCTGCCTCATATAGAGCAAGTAATGCTCTTGTATCACTACATAGGGTTCCGTTTAAGTTTCCTTGTTTATCAATGAATTCTTTAAATGCATCGCATGGCATGTAGCGCCGCTGCTGTCTTAGCAACCGGAATTGAAGGGAGATCGCATGGAAATCATCATTCGCAAACTTCACAGAAACTAGACTTTCTAGGGAGTTATCTATTTCTTCTTTAAAATGATAAGATACTCCAAGACGTTGAAGTGCATCGATAAGCTTCATTTTTGCAAATGGATTGAGGATGTCTACAAACATTTCCCTTGTTTCAACTATTAGGTCATCACATCTTTCCGTCATCCACTCCAGTGATTTCCGATAGTTATGAGGCAGTATTGGGTTCCTAATGAAGTAGTCACCCCACACACTCGACCTATAGTTTACAGCGTGGCGCTCCTCATCCACCACCCTATATCCTTGTGCGATCACTCTGCCGGCCATGTTGTTCTCTGCCAGCTGATCTATATGAACACTTACGATGTACTCTCTCTGTGGCTGAACTAACGAAGCTAGCTAGCTACGCCT

Coding Potentia
Explanation CPC Score
noncoding -1.3418
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0219600.2 3 17902778 A G
Osa03LNT0219600.2 3 17904396 T C
Osa03LNT0219600.2 3 17906384 T C
Osa03LNT0219600.2 3 17906360 T A
Osa03LNT0219600.2 3 17903579 T C
Osa03LNT0219600.2 3 17905537 A G
Osa03LNT0219600.2 3 17905541 C A
Osa03LNT0219600.2 3 17906070 G A
Osa03LNT0219600.2 3 17906425 T C
Osa03LNT0219600.2 3 17908773 G T
Osa03LNT0219600.2 3 17908776 T A
Osa03LNT0219600.2 3 17909213 T G
Osa03LNT0219600.2 3 17909771 A T
Osa03LNT0219600.2 3 17910141 T G
Osa03LNT0219600.2 3 17910440 A G
Osa03LNT0219600.2 3 17910970 A G
Osa03LNT0219600.2 3 17911150 A G
Osa03LNT0219600.2 3 17911448 C T
Osa03LNT0219600.2 3 17911591 T C
Osa03LNT0219600.2 3 17911625 C T
Osa03LNT0219600.2 3 17911930 T A
Osa03LNT0219600.2 3 17911941 A C
Osa03LNT0219600.2 3 17912065 A C
Osa03LNT0219600.2 3 17912092 A G
Osa03LNT0219600.2 3 17912471 T C
Osa03LNT0219600.2 3 17907969 T C
Osa03LNT0219600.2 3 17907614 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0219600.2 DTM_#DNAt_MULE_japo_Os0229 Chr3 - 17907416 17907935 519
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0219600.2 osa-miR5537 Cleavage 5.0 13.89 1 22
Osa03LNT0219600.2 osa-miR5537 Translation 4.0 16.647 1 22
Osa03LNT0219600.2 osa-miR5802 Translation 5.0 14.919 1 24
Osa03LNT0219600.2 osa-miR5816 Cleavage 4.0 13.638 1 24
Osa03LNT0219600.2 osa-miR5820 Cleavage 4.5 12.782 1 21
Osa03LNT0219600.2 osa-miR167a-3p Cleavage 5.0 10.357 1 22
Osa03LNT0219600.2 osa-miR395w Cleavage 5.0 15.732 1 22
Osa03LNT0219600.2 osa-miR1438 Cleavage 5.0 18.208 1 22
Osa03LNT0219600.2 osa-miR5155 Cleavage 5.0 9.588 1 24
Osa03LNT0219600.2 osa-miR172a Cleavage 5.0 11.122 1 21
Osa03LNT0219600.2 osa-miR172b Cleavage 5.0 11.122 1 21
Osa03LNT0219600.2 osa-miR172c Cleavage 4.0 11.122 1 21
Osa03LNT0219600.2 osa-miR172d-3p Cleavage 5.0 11.122 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0219600.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0219600.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0219600.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
Osa03LNT0219600.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0219600.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
Osa03LNT0219600.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0219600.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0219600.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0219600.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0219600.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0219600.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0219600.2 3 qDLR3 Resistance or Tolerance Other soil stress tolerance RM338 RM2453
Osa03LNT0219600.2 3 qGL3-1 Physiological trait Eating quality nan nan
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus